scholarly journals Systematic Evaluation of Immobilized Trypsin-Based Fast Protein Digestion for Deep and High-Throughput Bottom-Up Proteomics

PROTEOMICS ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 1700432 ◽  
Author(s):  
Xiaojing Shen ◽  
Liangliang Sun
Keyword(s):  
High Throughput ◽  
Systematic Evaluation ◽  
Protein Digestion ◽  
Bottom Up ◽  
Immobilized Trypsin

scholarly journals Luminex and Other Multiplex High Throughput Technologies for the Identification of, and Host Response to, Environmental Triggers of Type 1 Diabetes

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Sharad Purohit ◽  
Ashok Sharma ◽  
Jin-Xiong She
Keyword(s):  
Type 1 Diabetes ◽  
High Throughput ◽  
Host Response ◽  
Environmental Pollutants ◽  
Silent Period ◽  
Dietary Factors ◽  
Systematic Evaluation ◽  
Complex Nature ◽  
Diabetes Research

Complex interactions between a series of environmental factors and genes result in progression to clinical type 1 diabetes in genetically susceptible individuals. Despite several decades of research in the area, these interactions remain poorly understood. Several studies have yielded associations of certain foods, infections, and immunizations with the onset and progression of diabetes autoimmunity, but most findings are still inconclusive. Environmental triggers are difficult to identify mainly due to (i) large number and complex nature of environmental exposures, including bacteria, viruses, dietary factors, and environmental pollutants, (ii) reliance on low throughput technology, (iii) less efforts in quantifying host response, (iv) long silent period between the exposure and clinical onset of T1D which may lead to loss of the exposure fingerprints, and (v) limited sample sets. Recent development in multiplex technologies has enabled systematic evaluation of different classes of molecules or macroparticles in a high throughput manner. However, the use of multiplex assays in type 1 diabetes research is limited to cytokine assays. In this review, we will discuss the potential use of multiplex high throughput technologies in identification of environmental triggers and host response in type 1 diabetes.

Modular automated bottom-up proteomic sample preparation for high-throughput applications v1

2021 ◽  
Author(s):  
Yan Chen ◽  
Nurgul Kaplan Lease ◽  
Jennifer Gin ◽  
Tad Ogorzalek ◽  
Paul D. Adams ◽  
...  
Keyword(s):  
Sample Preparation ◽  
High Throughput ◽  
Tryptic Digestion ◽  
Gram Negative Bacteria ◽  
Bottom Up ◽  
Preparation Methods ◽  
Gram Negative ◽  
E Coli ◽  
Protocol Development ◽  
Set Up

Manual proteomic sample preparation methods limit sample throughput and often lead to poor data quality when thousands of samples must be analyzed. Automated workflows are increasingly used to overcome these issues for some (or even all) of the sample preparation steps. Here, we detail three optimised step-by-step protocols to: (A) lyse Gram-negative bacteria and fungal cells; (B) quantify the amount of protein extracted; and (C) normalize the amount of protein and set up tryptic digestion. These protocols have been developed to facilitate rapid, low variance sample preparation of hundreds of samples, be easily implemented on widely-available Beckman-Coulter Biomek automated liquid handlers, and allow flexibility for future protocol development. By using this workflow 50 micrograms of peptides for 96 samples can be prepared for tryptic digestion in under an hour. We validate these protocols by analyzing 47 E. coli and R. toruloides samples and show that this modular workflow provides robust, reproducible proteomic samples for high-throughput applications. The expected results from these protocols are 94 peptide samples from Gram-negative bacterial and fungal cells prepared for bottom-up quantitative proteomic analysis without the need for desalting column cleanup and with peptide variance (CVs) below 15%.

scholarly journals Characterization of Degraded Proteins in Paintings Using Bottom-Up Proteomic Approaches: New Strategies for Protein Digestion and Analysis of Data

2018 ◽  
Vol 90 (11) ◽  
pp. 6403-6408 ◽  
Author(s):  
Sibilla Orsini ◽  
Avinash Yadav ◽  
Marialaura Dilillo ◽  
Liam A. McDonnell ◽  
Ilaria Bonaduce
Keyword(s):  
Protein Digestion ◽  
Bottom Up ◽  
New Strategies

scholarly journals Construction of membrane-bound artificial cells using microfluidics: a new frontier in bottom-up synthetic biology

2016 ◽  
Vol 44 (3) ◽  
pp. 723-730 ◽  
Author(s):  
Yuval Elani
Keyword(s):  
Synthetic Biology ◽  
High Throughput ◽  
Lipid Membranes ◽  
Spatial Organization ◽  
Building Blocks ◽  
Artificial Cells ◽  
Bottom Up ◽  
Grand Challenges ◽  
New Frontier ◽  
Membrane Bound

The quest to construct artificial cells from the bottom-up using simple building blocks has received much attention over recent decades and is one of the grand challenges in synthetic biology. Cell mimics that are encapsulated by lipid membranes are a particularly powerful class of artificial cells due to their biocompatibility and the ability to reconstitute biological machinery within them. One of the key obstacles in the field centres on the following: how can membrane-based artificial cells be generated in a controlled way and in high-throughput? In particular, how can they be constructed to have precisely defined parameters including size, biomolecular composition and spatial organization? Microfluidic generation strategies have proved instrumental in addressing these questions. This article will outline some of the major principles underpinning membrane-based artificial cells and their construction using microfluidics, and will detail some recent landmarks that have been achieved.

scholarly journals Systematic Correlation Matrix Evaluation (SCoMaE) – A bottom-up, natural science-based approach to identify Indicators

2017 ◽  
Author(s):  
Nadine Mengis ◽  
David P. Keller ◽  
Andreas Oschlies
Keyword(s):  
Climate Change ◽  
Correlation Matrix ◽  
Expert Judgment ◽  
Comparative Assessment ◽  
Systematic Evaluation ◽  
Climate Change Scenarios ◽  
Scenario Simulation ◽  
Earth System ◽  
Bottom Up ◽  
The Earth

Abstract. This study introduces the Systematic Correlation Matrix Evaluation (SCoMaE) method, a bottom-up approach which combines expert judgment and statistical information to systematically select transparent, non redundant indicators for a com- prehensive assessment of the state of the Earth system. The methods consists of three basic steps: 1) Calculation of a correlation matrix among variables relevant for a given research question, 2) Systematic evaluation of the matrix, to identify clusters of variables with similar behavior and respective mutually independent indicators, and 3) Interpretation of the identified clusters, enabling a learning effect from the selection of indicators. Optional further analysis steps include: 4) Testing the robustness of identified clusters with respect to changes in forcing or boundary conditions, 5) Enabling a comparative assessment of varying scenarios by constructing and evaluating a common correlation matrix, or 6) Inclusion of expert judgment such as to prescribe indicators, to allow for considerations other than statistical consistency. The exemplary application of the SCoMaE method to Earth system model output forced by different CO2 emission scenarios reveals the necessity of re-evaluating indicators identified in a historical scenario simulation for an accurate assessment of an intermediate-high, as well as a business-as-usual, climate change scenario simulation, which arises from changes in prevailing correlations in the Earth system under varying climate forcing. For a comparative assessment of the three climate change scenarios, we construct and evaluate a common correlation matrix, in which we identify robust correlations between variables across the three considered scenarios.

Facile synthesis of enzyme–inorganic hybrid nanoflowers and their application as an immobilized trypsin reactor for highly efficient protein digestion

RSC Advances ◽  
2014 ◽  
Vol 4 (27) ◽  
pp. 13888-13891 ◽  
Author(s):  
Zian Lin ◽  
Yun Xiao ◽  
Ling Wang ◽  
Yuqing Yin ◽  
Jiangnan Zheng ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Immobilized Enzyme ◽  
Protein Digestion ◽  
Enzyme Reactor ◽  
Facile Synthesis ◽  
Inorganic Hybrid ◽  
Immobilized Enzyme Reactor ◽  
Highly Efficient ◽  
Novel Approach ◽  
Immobilized Trypsin

Hybrid nanoflowers were synthesized by a novel approach. The nanoflowers exhibited an enhanced enzymatic activity and can be used as an immobilized enzyme reactor (IMER) for highly efficient protein digestion.

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